UniProtKB - P38506 (XNI_ECOLI)
Protein
Flap endonuclease Xni
Gene
ygdG
Organism
Escherichia coli (strain K12)
Status
Functioni
Has flap endonuclease activity (PubMed:23821668), but does not seem to have exonuclease activity (PubMed:17567612 and PubMed:19000038). During DNA replication, flap endonucleases cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment.3 Publications
Caution
Was initially reported (PubMed:9592142) as a 3'-5' exonuclease due to contamination of samples. This protein possesses no such activity (PubMed:17567612 and PubMed:19000038).1 Publication
Cofactori
Protein has several cofactor binding sites:- Mg2+1 PublicationNote: Binds 2 Mg2+ per subunit. Only one magnesium ion has a direct interaction with the protein, the other interactions are indirect.1 Publication
- K+1 PublicationNote: Binds 1 K+ per subunit. The potassium ion strongly increases the affinity for DNA.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 104 | Magnesium | 1 | |
Metal bindingi | 171 | Potassium; via carbonyl oxygen | 1 | |
Metal bindingi | 172 | Potassium; via carbonyl oxygen | 1 | |
Metal bindingi | 180 | Potassium; via carbonyl oxygen | 1 | |
Metal bindingi | 182 | Potassium; via carbonyl oxygen | 1 | |
Metal bindingi | 185 | Potassium; via carbonyl oxygen | 1 |
GO - Molecular functioni
- 5'-flap endonuclease activity Source: UniProtKB
- DNA binding Source: UniProtKB
- magnesium ion binding Source: UniProtKB
- potassium ion binding Source: UniProtKB
GO - Biological processi
- DNA replication, Okazaki fragment processing Source: UniProtKB
Keywordsi
Molecular function | DNA-binding, Endonuclease, Hydrolase, Nuclease |
Ligand | Magnesium, Metal-binding, Potassium |
Enzyme and pathway databases
BioCyci | EcoCyc:EG12372-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: Flap endonuclease Xni (EC:3.1.-.-)Short name: FEN Alternative name(s): Exonuclease IX Short name: ExoIX |
Gene namesi | Name:ygdG Synonyms:exo, xni Ordered Locus Names:b2798, JW5446 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Disruption phenotypei
Can be deleted, however double-disruptions of polA and xni are not viable, suggesting they have a redundant essential function.1 Publication
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 67 | K → A: Strongly reduces flap endonuclease activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000101292 | 1 – 251 | Flap endonuclease XniAdd BLAST | 251 |
Proteomic databases
jPOSTi | P38506 |
PaxDbi | P38506 |
PRIDEi | P38506 |
Interactioni
Subunit structurei
Interacts with the DNA-binding proteins SSB and H-NS.
1 PublicationProtein-protein interaction databases
BioGRIDi | 4259222, 102 interactors 851586, 1 interactor |
DIPi | DIP-11145N |
IntActi | P38506, 3 interactors |
STRINGi | 511145.b2798 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 160 – 249 | 5'-3' exonucleaseSequence analysisAdd BLAST | 90 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 184 – 189 | Interaction with DNA | 6 |
Coiled coil
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Coiled coili | 198 – 225 | Sequence analysisAdd BLAST | 28 |
Sequence similaritiesi
Belongs to the Xni family.Curated
Keywords - Domaini
Coiled coilPhylogenomic databases
eggNOGi | COG0258, Bacteria |
HOGENOMi | CLU_004675_1_2_6 |
InParanoidi | P38506 |
PhylomeDBi | P38506 |
Family and domain databases
CDDi | cd09898, H3TH_53EXO, 1 hit |
HAMAPi | MF_01192, Xni, 1 hit |
InterProi | View protein in InterPro IPR020046, 5-3_exonucl_a-hlix_arch_N IPR002421, 5-3_exonuclease IPR036279, 5-3_exonuclease_C_sf IPR020045, DNA_polI_H3TH IPR038969, FEN IPR008918, HhH2 IPR029060, PIN-like_dom_sf IPR022895, Xni |
PANTHERi | PTHR42646, PTHR42646, 1 hit |
Pfami | View protein in Pfam PF01367, 5_3_exonuc, 1 hit PF02739, 5_3_exonuc_N, 1 hit |
SMARTi | View protein in SMART SM00475, 53EXOc, 1 hit SM00279, HhH2, 1 hit |
SUPFAMi | SSF47807, SSF47807, 1 hit SSF88723, SSF88723, 1 hit |
i Sequence
Sequence statusi: Complete.
P38506-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MAVHLLIVDA LNLIRRIHAV QGSPCVETCQ HALDQLIMHS QPTHAVAVFD
60 70 80 90 100
DENRSSGWRH QRLPDYKAGR PPMPEELHDE MPALRAAFEQ RGVPCWSTSG
110 120 130 140 150
NEADDLAATL AVKVTQAGHQ ATIVSTDKGY CQLLSPTLRI RDYFQKRWLD
160 170 180 190 200
APFIDKEFGV QPQQLPDYWG LAGISSSKVP GVAGIGPKSA TQLLVEFQSL
210 220 230 240 250
EGIYENLDAV AEKWRKKLET HKEMAFLCRD IARLQTDLHI DGNLQQLRLV
R
Sequence cautioni
The sequence AAB40448 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated
The sequence BAE76870 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L07763 Genomic DNA No translation available. U29581 Genomic DNA Translation: AAB40448.1 Different initiation. U00096 Genomic DNA Translation: AAC75840.2 AP009048 Genomic DNA Translation: BAE76870.1 Different initiation. M27177 Genomic DNA No translation available. |
PIRi | B65062 |
RefSeqi | NP_417278.4, NC_000913.3 WP_000268232.1, NZ_SSUV01000026.1 |
Genome annotation databases
EnsemblBacteriai | AAC75840; AAC75840; b2798 BAE76870; BAE76870; BAE76870 |
GeneIDi | 57730398 947256 |
KEGGi | ecj:JW5446 eco:b2798 |
PATRICi | fig|1411691.4.peg.3935 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L07763 Genomic DNA No translation available. U29581 Genomic DNA Translation: AAB40448.1 Different initiation. U00096 Genomic DNA Translation: AAC75840.2 AP009048 Genomic DNA Translation: BAE76870.1 Different initiation. M27177 Genomic DNA No translation available. |
PIRi | B65062 |
RefSeqi | NP_417278.4, NC_000913.3 WP_000268232.1, NZ_SSUV01000026.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3ZD8 | X-ray | 2.00 | A/B | 1-251 | [»] | |
3ZD9 | X-ray | 2.00 | A | 1-251 | [»] | |
3ZDA | X-ray | 1.50 | A | 1-251 | [»] | |
3ZDB | X-ray | 1.47 | A | 1-251 | [»] | |
3ZDC | X-ray | 1.53 | A | 1-251 | [»] | |
3ZDD | X-ray | 1.50 | A | 1-251 | [»] | |
3ZDE | X-ray | 2.45 | A | 1-251 | [»] | |
SMRi | P38506 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4259222, 102 interactors 851586, 1 interactor |
DIPi | DIP-11145N |
IntActi | P38506, 3 interactors |
STRINGi | 511145.b2798 |
Proteomic databases
jPOSTi | P38506 |
PaxDbi | P38506 |
PRIDEi | P38506 |
Genome annotation databases
EnsemblBacteriai | AAC75840; AAC75840; b2798 BAE76870; BAE76870; BAE76870 |
GeneIDi | 57730398 947256 |
KEGGi | ecj:JW5446 eco:b2798 |
PATRICi | fig|1411691.4.peg.3935 |
Organism-specific databases
EchoBASEi | EB2275 |
Phylogenomic databases
eggNOGi | COG0258, Bacteria |
HOGENOMi | CLU_004675_1_2_6 |
InParanoidi | P38506 |
PhylomeDBi | P38506 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG12372-MONOMER |
Miscellaneous databases
PROi | PR:P38506 |
Family and domain databases
CDDi | cd09898, H3TH_53EXO, 1 hit |
HAMAPi | MF_01192, Xni, 1 hit |
InterProi | View protein in InterPro IPR020046, 5-3_exonucl_a-hlix_arch_N IPR002421, 5-3_exonuclease IPR036279, 5-3_exonuclease_C_sf IPR020045, DNA_polI_H3TH IPR038969, FEN IPR008918, HhH2 IPR029060, PIN-like_dom_sf IPR022895, Xni |
PANTHERi | PTHR42646, PTHR42646, 1 hit |
Pfami | View protein in Pfam PF01367, 5_3_exonuc, 1 hit PF02739, 5_3_exonuc_N, 1 hit |
SMARTi | View protein in SMART SM00475, 53EXOc, 1 hit SM00279, HhH2, 1 hit |
SUPFAMi | SSF47807, SSF47807, 1 hit SSF88723, SSF88723, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | XNI_ECOLI | |
Accessioni | P38506Primary (citable) accession number: P38506 Secondary accession number(s): Q2MA36, Q46922 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 1, 1994 |
Last sequence update: | November 24, 2009 | |
Last modified: | February 10, 2021 | |
This is version 152 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families